7-129434483-C-A

Variant names:

• chr7-129434483-C-A
• rs1348518896
• NM_020704.3:c.11C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020704.3(STRIP2):​c.11C>A​(p.Pro4His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P4S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: STRIP2 NM_020704.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 1 publications found

Genes affected

STRIP2 (HGNC:22209): (striatin interacting protein 2) Involved in cell migration; cytoskeleton organization; and regulation of cell shape. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

STRIP2 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000300026 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07939017).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020704.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP2	NM_020704.3	MANE Select	c.11C>A	p.Pro4His	missense	Exon 1 of 21	NP_065755.1	Q9ULQ0-1
	STRIP2	NM_001134336.2		c.11C>A	p.Pro4His	missense	Exon 1 of 20	NP_001127808.1	Q9ULQ0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STRIP2	ENST00000249344.7	TSL:1 MANE Select	c.11C>A	p.Pro4His	missense	Exon 1 of 21	ENSP00000249344.2	Q9ULQ0-1
	STRIP2	ENST00000435494.2	TSL:1	c.11C>A	p.Pro4His	missense	Exon 1 of 20	ENSP00000392393.2	Q9ULQ0-2
	STRIP2	ENST00000947594.1		c.11C>A	p.Pro4His	missense	Exon 1 of 21	ENSP00000617653.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1362268 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 671036

African (AFR) AF: 0.00 AC: 0 AN: 28720

American (AMR) AF: 0.00 AC: 0 AN: 34400

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24420

East Asian (EAS) AF: 0.00 AC: 0 AN: 33488

South Asian (SAS) AF: 0.00 AC: 0 AN: 76894

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33356

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4030

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1070102

Other (OTH) AF: 0.00 AC: 0 AN: 56858

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	14
DANN	Benign	0.94
DEOGEN2	Benign	0.0071	T
Eigen	Benign	-0.83
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.59	T
M_CAP	Benign	0.077	D
MetaRNN	Benign	0.079	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.24
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-0.75	N
REVEL	Benign	0.14
Sift	Benign	0.17	T
Sift4G	Uncertain	0.026	D
Polyphen		0.89	P
Vest4		0.20
MutPred		0.067		Loss of catalytic residue at P4 (P = 0.1049)
MVP		0.15
MPC		0.25
ClinPred		0.49	T
GERP RS		2.7
PromoterAI		0.034	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1
Varity_R		0.069
gMVP		0.23
Mutation Taster		=96/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1348518896; hg19: chr7-129074324;